That decision opened a split between Merkel's Christian Democrats and the Christian Social Union, parties that have been in partnership since 1949.
If Merkel holds firm and Seehofer does quit, the CSU could offer a replacement interior minister if it aims to remain tied to her party.
Last November, when Merkel was negotiating her fourth coalition, the long-time chancellor told German broadcaster ZDF she was "very sceptical" about leading a minority government and would rather call new elections.
They argued such zones would not limit the number of migrants given that most were fleeing wars in the Middle East and Afghanistan and therefore entitled to asylum in Germany.
Despite those steps, both sister parties took a beating in September 2017 elections as millions of voters switched to the far-right AfD party, which is also running against the CSU in Bavarian elections in October, threatening to destroy its governing majority.
Following marathon talks at the Brussels summer summit, European leaders eventually reached a compromise on migration in the early hours of Friday.
It was reported that Merkel had believed that the European solution could satisfy CSU's ultimatum, which was due on Sunday, otherwise Seehofer would bypass Merkel to implement a tougher asylum policy.
Merkel, Seehofer, Nahles and senior members of their parties met in the chancellery on Tuesday evening to discuss the plan.
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Zlatko Dalic opted for Modric, Rakitic and Marcelo Brozovic, with Mateo Kovacic initially on the bench. Kjaer blasted home for the Danes before Kramaric kept his cool to beat Schmeichel from the spot.
"She's switched camp from the moderates in the government coalition, left the SPD and is now joining the CSU, but by this she has lot a lost of her credibility within the coalition party and also in public opinion".
Seehofer wants to turn back at the border asylum-seekers who have already registered in another European Union country but Merkel is adamant that Germany shouldn't take unilateral actions that affect other EU nations.
Merkel, who has been in office since 2005, warned last week the battle over migration could decide the EU's future.
In high-stakes crisis talks on Monday, Ms. Merkel put to rest for now a unsafe row with a longtime rival, Interior Minister Horst Seehofer, that had threatened the survival of her shaky 100-day-old coalition.
Nonetheless, for now the deal suggested that Merkel - in power for over 12 years, and the EU's longest serving leader - goes on to live another day after surviving the latest bruising challenge to her authority.
The sources said that in Sunday's private party meeting, Seehofer said he had a "conversation with no effect" with Merkel when they held talks on Saturday about the European Union migration deal, AFP news agency reported.
The "Union" of CDU and CSU have blended the southern state's beer-and-lederhosen-infused conservatism with more moderate politics, forming a centre-right force that dominated Germany for decades.
Seehofer will attempt last-ditch talks with Merkel on Monday, but the discussions will be taking place in an increasingly antagonistic atmosphere.